3B0V - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   TRNA-DIHYDROURIDINE SYNTHASE FROM THERMUS THERMOPHILUS IN COMPLEX WITH TRNA

Authors :   F. Yu, Y. Tanaka, K. Yamashita, A. Nakamura, M. Yao, I. Tanaka

Date :   14 Jun 11 (Deposition) - 14 Dec 11 (Release) - 21 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.51

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Tim Barrel, Oxidoreductase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Yu, Y. Tanaka, K. Yamashita, T. Suzuki, A. Nakamura, N. Hirano, T. Suzuki, M. Yao, I. Tanaka
Molecular Basis Of Dihydrouridine Formation On Trna
Proc. Natl. Acad. Sci. Usa V. 108 19593 2011
PubMed-ID: 22123979 | Reference-DOI: 10.1073/PNAS.1112352108

Molecule 1 - TRNA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC19
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

Molecule 2 - TRNA-DIHYDROURIDINE SYNTHASE
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	CDFDUET-1
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TTHA0016
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 24)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	H2U	2	Mod. Nucleotide	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
3	MSE	20	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	H2U	1	Mod. Nucleotide	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	H2U	1	Mod. Nucleotide	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	H2U A:20 , ALA C:9 , PRO C:10 , MSE C:11 , VAL C:12 , MSE C:36 , GLN C:63 , ASN C:90 , LYS C:132 , HIS C:164 , ARG C:178 , ASN C:203 , GLY C:205 , GLY C:225 , ARG C:226	BINDING SITE FOR RESIDUE FMN C 400
2	AC2	SOFTWARE	H2U B:20 , ALA D:9 , PRO D:10 , MSE D:11 , VAL D:12 , MSE D:36 , GLN D:63 , ASN D:90 , LYS D:132 , HIS D:164 , ARG D:178 , ASN D:203 , GLY D:204 , GLY D:205 , GLY D:225 , ARG D:226	BINDING SITE FOR RESIDUE FMN D 400

(no "SS Bond" information available for 3B0V)

Asymmetric Unit

No.	Residues
1	His C:58	-	Pro C:59
2	His D:58	-	Pro D:59

(no "SAP(SNP)/Variant" information available for 3B0V)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0034	PS01136	Uncharacterized protein family UPF0034 signature.	DUSAL_THET8	87-105	2	C:87-105 D:87-105

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0034	PS01136	Uncharacterized protein family UPF0034 signature.	DUSAL_THET8	87-105	1	C:87-105 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0034	PS01136	Uncharacterized protein family UPF0034 signature.	DUSAL_THET8	87-105	1	- D:87-105

(no "Exon" information available for 3B0V)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:RNA  Length:73
                                                                                                         
                 3b0v A   1 GCCGAGGUAGCUCAGUUGGuAGAGCAUGCGACUGAAAAUCGCAGUGUCGGCGGUUCGAUUCCGCCCCUCGGCA  73
                                    10        20        30        40        50        60        70   
                                              20-H2U

Chain B from PDB  Type:RNA  Length:73
                                                                                                         
                 3b0v B   1 GCCGAGGUAGCUCAGUUGGuAGAGCAUGCGACUGAAAAUCGCAGUGUCGGCGGUUCGAUUCCGCCCCUCGGCA  73
                                    10        20        30        40        50        60        70   
                                              20-H2U

Chain C from PDB  Type:PROTEIN  Length:315
 aligned with DUSAL_THET8 | Q5SMC7 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:315
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     
          DUSAL_THET8     1 MLDPRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLALSTKANREIPPLRHDWVHRLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRPSRLEVARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLSEGRSLQALDRALRLMEEE 315
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.......hhhhhhhhhhhh...eee...eehhhhhhhhhhhhhh.hhhhh.eeeeee..hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhh...eeeee...................hhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------UPF0034            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b0v C   1 mLDPRLSVAPmVDRTDRHFRFLVRQVSLGVRLYTEmTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAmGEAVRVPVTVKmRLGLEGKETYRGLAQSVEAmAEAGVKVFVVHARSALLALSTKANREIPPLRHDWVHRLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVmLGRAVYEDPFVLEEADRRVFGLPRRPSRLEVARRmRAYLEEEVLKGTPPWAVLRHmLNLFRGRPKGRLWRRLLSEGRSLQALDRALRLmEEE 315
                            |       10|       20        30     |  40        50        60        70        80        90       100       110       120|      130  |    140       150  |    160       170       180       190       200       210       220  |    230       240       250       260       270       280       290       300       310 |   
                            |        11-MSE                   36-MSE                                                                              121-MSE     133-MSE             153-MSE                                                               223-MSE                            258-MSE              279-MSE                          312-MSE
                            1-MSE

Chain D from PDB  Type:PROTEIN  Length:315
 aligned with DUSAL_THET8 | Q5SMC7 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:315
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     
          DUSAL_THET8     1 MLDPRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLALSTKANREIPPLRHDWVHRLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRPSRLEVARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLSEGRSLQALDRALRLMEEE 315
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.......hhhhhhhhhhhh....ee...eehhhhhhhhhhhhhh.hhhhh.eeeeee..hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeeee..........hhhhh....hhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------UPF0034            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b0v D   1 mLDPRLSVAPmVDRTDRHFRFLVRQVSLGVRLYTEmTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAmGEAVRVPVTVKmRLGLEGKETYRGLAQSVEAmAEAGVKVFVVHARSALLALSTKANREIPPLRHDWVHRLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVmLGRAVYEDPFVLEEADRRVFGLPRRPSRLEVARRmRAYLEEEVLKGTPPWAVLRHmLNLFRGRPKGRLWRRLLSEGRSLQALDRALRLmEEE 315
                            |       10|       20        30     |  40        50        60        70        80        90       100       110       120|      130  |    140       150  |    160       170       180       190       200       210       220  |    230       240       250       260       270       280       290       300       310 |   
                            |        11-MSE                   36-MSE                                                                              121-MSE     133-MSE             153-MSE                                                               223-MSE                            258-MSE              279-MSE                          312-MSE
                            1-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3B0V)

(no "CATH Domain" information available for 3B0V)

(no "Pfam Domain" information available for 3B0V)

Asymmetric Unit(hide GO term definitions)

Chain C,D (DUSAL_THET8 | Q5SMC7)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0017150	tRNA dihydrouridine synthase activity	Catalysis of the reaction: tRNA-uracil + acceptor = tRNA-dihydrouridine + reduced acceptor.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0002943	tRNA dihydrouridine synthesis	The process whereby a uridine in a transfer RNA is converted to dihydrouridine.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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	DUSAL_THET8 \| Q5SMC7	:	3b0p 3b0u

3b0p	APO FORM
3b0u	FRAGMENT COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 24)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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